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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Developing Bloom Filters for Web Archives’ Holdings (Final Project Report)

The main goal of the project was to develop a framework for web archives to create Bloom filters based on their holdings of archived web resources. A Bloom filter (BF) is a data structure that, in our scenario, contains hash values of all (or a subset of) URLs, of which an archive has one or more archival copies. Two main use cases fall in scope for this project and are supported by a BF implementation: 1) Sharing of an archive’s holdings (URLs) and 2) Querying the holdings of one or more archives. Since URL strings are hashed before ingested into the BF, the index of an archive is not shared in plain text when the BF is shared with trusted parties. On the other hand, a BF implementation does allow queries for a URL to confirm if an archive indeed has one or more archival copies of that URL. This collaborative project between Los Alamos National Laboratory (LANL) and the Croatian Web Archive (HAW), from the National and University Library in Zagreb (NSK), developed by NSK and University of Zagreb University Computing Center SRCE), aimed at developing software to create BFs, evaluate the scalability of the approach, pilot a search service based on BFs, and design a framework for archives to share their filters with trusted parties. In the remainder of this document, we will report on the work completed with respect to the individual deliverables, outline aspects of future work, and conclude with our recommendations for the use of BFs for the web archiving community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Bloom Filter framework for Web Archives

The software provides a framework to build a fast look up layer that reflects the holdings of an archive or database and operates between search/discovery system and disk storage. The software utilizes Bloom filter (BF) data structure. The discovery service powered by the Bloom filter layer comes with a very high level of accuracy yet space-saving, since BF compresses data to fit into RAM.

Balakireva, Lyudmila↗
DOE OSTI2022

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗